Describing California Bay-Delta Communities following Invasion of Water Primrose
DNA was extracted from the sediment using with the QIAGEN PowerSoil Pro Kit. We used Qiagen multiplex PCR mastermix to amplify the 16S, 18S, PITS, FITS, CO1, and 12S markers; with each sample having 3 replicates per marker. We then pooled these replicates and cleaned with MagBio HighPrep PCR magnetic beads. We quantified the PCR products on a Thermo Scientific Varioskan Lux multimode microplate reader (Thermo Scientific), before pooling equimolar amount of each amplicon per sample. We indexed our libraries with KAPA HiFi HotStart ReadyMix and Nextera indicies, and bead-cleaned at a 1.1:1 bead to library ratio. We sequenced our libraries to a minimum read depth of 125,000 reads. Some samples did not meet this threshold, and thus were repooled and resequenced as above.